added back together corrected compose files

SevKohler · May 29, 2024 · 11f8ca5 · 11f8ca5
1 parent 1e2b698
commit 11f8ca5
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Showing 8 changed files with 70 additions and 19 deletions.
diff --git a/docker/docker-compose-ehrbase.yml b/docker/docker-compose-ehrbase.yml
@@ -9,7 +9,7 @@ services:
     networks:
       - ehrbase-net
     environment:
-      DB_URL: jdbc:postgresql://ehrdb:5433/ehrbase
+      DB_URL: jdbc:postgresql://ehrdb:5432/ehrbase
       DB_USER_ADMIN: ehrbase
       DB_PASS_ADMIN: ehrbase
       SECURITY_AUTHTYPE: BASIC
@@ -20,7 +20,8 @@ services:
       DB_USER: ehrbase_restricted
       DB_PASS: ehrbase_restricted
     depends_on:
-      - ehrdb
+      ehrdb:
+        condition: service_healthy
     restart: on-failure
 
   ehrdb:
@@ -32,10 +33,21 @@ services:
     environment:
       POSTGRES_USER: postgres
       POSTGRES_PASSWORD: postgres
+      PGDATA: /var/lib/postgresql/data/pgdata
       EHRBASE_USER_ADMIN: ehrbase
       EHRBASE_PASSWORD_ADMIN: ehrbase
       EHRBASE_USER: ehrbase_restricted
       EHRBASE_PASSWORD: ehrbase_restricted
+    volumes:
+      - ehrdb-pgdata:/var/lib/postgresql/data/pgdata
+    healthcheck:
+      test: "pg_isready -h localhost -U $$POSTGRES_USER"
+      interval: 10s
+      timeout: 5s
+      retries: 70
 
 networks:
   ehrbase-net: {}
+
+volumes:
+  ehrdb-pgdata:
diff --git a/docker/docker-compose-full.yml b/docker/docker-compose-full.yml
@@ -1,6 +1,5 @@
 #docker-compose-full.yml
 services:
-
   ehrbase:
     image: ehrbase/ehrbase:next
     ports:
@@ -19,7 +18,8 @@ services:
       DB_USER: ehrbase_restricted
       DB_PASS: ehrbase_restricted
     depends_on:
-      - ehrdb
+      ehrdb:
+        condition: service_healthy
     restart: on-failure
 
   ehrdb:
@@ -31,10 +31,18 @@ services:
     environment:
       POSTGRES_USER: postgres
       POSTGRES_PASSWORD: postgres
+      PGDATA: /var/lib/postgresql/data/pgdata
       EHRBASE_USER_ADMIN: ehrbase
       EHRBASE_PASSWORD_ADMIN: ehrbase
       EHRBASE_USER: ehrbase_restricted
       EHRBASE_PASSWORD: ehrbase_restricted
+    volumes:
+      - ehrdb-pgdata:/var/lib/postgresql/data/pgdata
+    healthcheck:
+      test: "pg_isready -h localhost -U $$POSTGRES_USER"
+      interval: 10s
+      timeout: 5s
+      retries: 70
 
   aft:
     image: aft:latest
@@ -78,11 +86,23 @@ services:
     environment:
       POSTGRES_USER: postgres
       POSTGRES_PASSWORD: postgres
+      PGDATA: /var/lib/postgresql/data/pgdata
       EHRBASE_USER_ADMIN: ehrbase
       EHRBASE_PASSWORD_ADMIN: ehrbase
       EHRBASE_USER: ehrbase_restricted
       EHRBASE_PASSWORD: ehrbase_restricted
     command: -p 5433
+    volumes:
+      - ehrdb2-pgdata:/var/lib/postgresql/data/pgdata
+    healthcheck:
+      test: "pg_isready -h localhost -U $$POSTGRES_USER"
+      interval: 10s
+      timeout: 5s
+      retries: 70
 
 networks:
   ehrbase-net: {}
+
+volumes:
+  ehrdb-pgdata:
+  ehrdb2-pgdata:
diff --git a/docker/docker-compose-without-aft.yml b/docker/docker-compose-without-aft.yml
@@ -1,6 +1,5 @@
 #docker-compose-full.yml
 services:
-
   ehrbase:
     image: ehrbase/ehrbase:next
     ports:
@@ -19,8 +18,10 @@ services:
       DB_USER: ehrbase_restricted
       DB_PASS: ehrbase_restricted
     depends_on:
-      - ehrdb
+      ehrdb:
+        condition: service_healthy
     restart: on-failure
+
   ehrdb:
     image: ehrbase/ehrbase-postgres:latest
     ports:
@@ -30,10 +31,18 @@ services:
     environment:
       POSTGRES_USER: postgres
       POSTGRES_PASSWORD: postgres
+      PGDATA: /var/lib/postgresql/data/pgdata
       EHRBASE_USER_ADMIN: ehrbase
       EHRBASE_PASSWORD_ADMIN: ehrbase
       EHRBASE_USER: ehrbase_restricted
       EHRBASE_PASSWORD: ehrbase_restricted
+    volumes:
+      - ehrdb-pgdata:/var/lib/postgresql/data/pgdata
+    healthcheck:
+      test: "pg_isready -h localhost -U $$POSTGRES_USER"
+      interval: 10s
+      timeout: 5s
+      retries: 70
 
   ehrbase2:
     image: ehrbase/ehrbase:next
@@ -65,11 +74,23 @@ services:
     environment:
       POSTGRES_USER: postgres
       POSTGRES_PASSWORD: postgres
+      PGDATA: /var/lib/postgresql/data/pgdata
       EHRBASE_USER_ADMIN: ehrbase
       EHRBASE_PASSWORD_ADMIN: ehrbase
       EHRBASE_USER: ehrbase_restricted
       EHRBASE_PASSWORD: ehrbase_restricted
     command: -p 5433
+    volumes:
+      - ehrdb2-pgdata:/var/lib/postgresql/data/pgdata
+    healthcheck:
+      test: "pg_isready -h localhost -U $$POSTGRES_USER"
+      interval: 10s
+      timeout: 5s
+      retries: 70
 
 networks:
   ehrbase-net: {}
+
+volumes:
+  ehrdb-pgdata:
+  ehrdb2-pgdata:
diff --git a/src/main/java/org/bih/aft/controller/QueryController.java b/src/main/java/org/bih/aft/controller/QueryController.java
@@ -6,9 +6,6 @@
 import org.bih.aft.exceptions.InvalidCountQuery;
 import org.bih.aft.controller.dao.AQLinput;
 import org.bih.aft.ports.QueryUseCase;
-import org.bih.aft.service.FederationService;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
 import org.springframework.http.HttpStatus;
 import org.springframework.http.ResponseEntity;
 import org.springframework.web.bind.annotation.*;

diff --git a/src/main/java/org/bih/aft/service/CountVerificator.java b/src/main/java/org/bih/aft/service/CountVerificator.java
@@ -7,10 +7,14 @@
 import org.ehrbase.openehr.sdk.aql.dto.operand.AggregateFunction;
 import org.ehrbase.openehr.sdk.aql.dto.select.SelectClause;
 import org.ehrbase.openehr.sdk.aql.dto.select.SelectExpression;
+import org.springframework.stereotype.Service;
 
 import java.util.List;
 @Slf4j
+@Service
 public class CountVerificator implements QueryVerificator {
+
+
     @Override
     public void verify(AQLinput aqlQuery) { // TODO: What return type here ? Response should be 400 in the end
         String query = aqlQuery.aql();

diff --git a/src/main/java/org/bih/aft/service/FederationListService.java b/src/main/java/org/bih/aft/service/FederationListService.java
@@ -7,6 +7,7 @@
 
 import java.io.File;
 import java.io.IOException;
+import java.io.InputStream;
 import java.util.List;
 
 @Service
@@ -18,10 +19,8 @@ public class FederationListService implements LocationProvider {
 
     private FederationList loadFederationfile() {
         ObjectMapper mapper = new ObjectMapper();
-        ClassLoader classloader = Thread.currentThread().getContextClassLoader();
-        File file = new File(classloader.getResource(federationListPath).getFile());
-        try {
-            federationList = mapper.readValue(file, FederationList.class);
+        try(InputStream inputStream = getClass().getClassLoader().getResourceAsStream(federationListPath)){
+            federationList = mapper.readValue(inputStream, FederationList.class);
         } catch (IOException e) {
             throw new RuntimeException(e);
         }

diff --git a/src/main/java/org/bih/aft/service/FederationService.java b/src/main/java/org/bih/aft/service/FederationService.java
@@ -25,14 +25,13 @@ public class FederationService implements QueryUseCase {
     @Value("${aft.location}")
     private String homeLocation;
 
-    OpenEhrClient openEhrClient;
+    private final OpenEhrClient openEhrClient;
 
-    QueryVerificator queryVerificator;
+    private final QueryVerificator queryVerificator;
 
-    LocationProvider federationListService;
-
-    QueryService queryService;
+    private final LocationProvider federationListService;
 
+    private final QueryService queryService;
 
     @Override
     public List<FeasibilityOutput> federate(AQLinput aqlQuery) throws InvalidCountQuery {

diff --git a/src/test/java/org/bih/aft/service/FederationListServiceTest.java b/src/test/java/org/bih/aft/service/FederationListServiceTest.java
@@ -16,7 +16,6 @@ void getFederationList() {
         List<Location> actual = service.locations();
         Location location = new Location("Test2", "https://localhost:8091");
         List<Location> expected = Lists.list(location);
-
         assertEquals(expected, actual);
     }
 }